Asthma is the most common disease of childhood in the United States. The role of microbial flora and allergens in asthma development is poorly understood. We found reduced pro-inflammatory Th2 cytokine production at age 2, reduced risk of eczema, and subsequent reduced allergy/allergic rhinitis risk by age 7 in children with elevated levels in infancy of home endotoxin, the biologically active form of lipopolysaccharide (LPS) contained in the outer membrane of gram-negative bacteria. In contrast, elevated early- life levels of dust mite increased allergic sensitization and active asthma risk;elevated home fungal levels in infancy increased allergic rhinitis risk. Endotoxin was correlated with other microbial flora (e.g., muramic acid, a marker for gram + bacteria, fungi);it may be a marker for an array of exposures recognized by antigen presenting cells (APCs) as pathogen-associated-molecular patterns (PAMPS). Ligation of PAMPS to innate APCs or regulatory cells may result in downregulation of allergic adaptive immune responses, or may result in airway inflammation depending on dose, timing and genes. In preliminary analyses, elevated muramic acid and elevated endotoxin were both linked to asthma symptom protection at age 7, though paradoxically, endotoxin predicted increased infant wheeze. We propose to extend our prospective longitudinal study of children of asthmatic/allergic parents to examine multiple microbial PAMP influences on asthma and immune development, following our birth cohort through the early teen years, a period of significant transition for allergy and asthma. We hypothesize that by the early teen years: (1) Early life exposure to home endotoxin will be associated with protection against allergic rhinitis and allergic sensitization. The relationship of endotoxin to wheeze, asthma and the secondary phenotypes of airway obstruction and airway inflammation, will be dependent on dose, timing, persistence of exposure, and host factors. As a marker for multiple PAMPS, endotoxin will be correlated with muramic acid, which will have similar effects on allergic rhinitis, wheeze, asthma and allergic sensitization. (2) Early life exposure to home fungi will be a risk factor for allergic rhinitis, wheeze, asthma and allergic sensitization. Fungal irritant and allergenic effects will dominate over the potential protective effects of fungi as PAMPS. (3) Reduction in bacterial PAMP exposures will be linked to reduced innate (TLR2, TLR4, MyD88, sCD14, IL-12) and regulatory (foxp3, IL-10, TGF-[unreadable]) gene expression and cytokine production, which in turn will lead to reduced adaptive Th1 (IFN-[unreadable]) cytokine production, elevated pro-allergic Th2 (IL-4, IL-13) cytokine production and subsequent allergic sensitization. Understanding the evolution of the allergic immune response to microbial flora and correlated cofactors is an important key to developing better environmental or pharmacologic controls to either prevent or switch off the tendency to allergy and asthma in childhood.